fiber.angle: Calculating the orientation of muscle fibers

In GoodFibes: Detection and Reconstruction of Muscle Fibers from diceCT Image Data

Calculating the orientation of muscle fibers

Description

Calculating the orientation or pennation angle of individual muscle fibers. This function can calculate fiber angles around a central axis (x, y or z) or in reference to a particular "view" (plane). Fiber data can optionally be aligned to a line of action (tendon, line between origin and insertion points, etc.) to calculate pennation angle.

Usage

fiber.angle(fib.list, axis, reference = "axis", 
endpoints=NULL, end.to.end=FALSE)

Arguments

fib.list	A list of muscle fiber paths generated by good.fibes or from the various cleaning and processing function (must contain $fiber.points).
axis	The axis around which angles will be calculated as a deviation from. Default is 3 (z). This axis is treated as the "z" axis for "plane" options.
reference	Should the orientation angles be calculated about an axis (specified by "axis") or in reference to a plane ("plane.xz" "plane.yz", or "plane.xy", where z is the value of "axis"). When calculating pennation angles, reference = "line.of.action" and argument "endpoints" should be supplied.
endpoints	An optional 2X3 matrix generated by find.endpoints. When supplied, data is centered on the first endpoint and rotated such that the second lies along the z axis, such that angles are calculated in reference to a straight line between the two endpoints.
end.to.end	Should the angle be calculated over the entire fiber (FALSE) or based on just the enpoints of the fiber (TRUE).

Details

Fiber angle is calculated from the eigenvectors of a Principal Component Analysis of the fiber coordindates using prcomp.

Value

A vector of angles in degrees corresponding to each fiber in the original list

Author(s)

J. Arbour

References

Arbour, J. 2023. GoodFibes: an R package for the detection of muscle fibers from diceCT scans. Integrative Organismal Biology 5(1): obad030.

Katzke, J., Puchenkov, P., Stark, H., and Economo, E. 2022. A Roadmap to Reconstructing Muscle Architecture from CT Data. Integrative Organismal Biology 4(1): 1-16.

Sullivan, S., McGechie, F., Middleton, K., and Holliday, C. 3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris).Integrative Organismal Biology 1(1):1-18.

See Also

fiber.lengths

Examples

olddir<-getwd()

data(ant.final)
fangle<-fiber.angle(ant.final,3)
fangle

cols<-color.scale(fangle, c("blue", "red"))
muscle.plot.stl(ant.final, cols=cols, df = 1)

setwd(olddir)

GoodFibes documentation built on April 27, 2026, 9:09 a.m.